what hurts the most
by Celticsfangirl
Summary: My take on what happened after the shooting in the warehouse. Jane gets a job offer from Chicago and decides to leave BPD to take it. Jane tries to apologize to Maura one more time but what happens changes their relationship even more than it already has.
1. Chapter 1 Resigning

_**Chapter One- Resigning**_

Jane hadn't slept properly in months since the shooting at the warehouse. The nights were long and unbearable, and the days were even worse. The months of apologizing were not accepted, but instead were met with harsh, cold words. It had been weeks of self-hatred, guilt, and regret. The more she tried to apologize the less Maura forgave her, Jane finally realized that Maura would probably never forgive her. Their friendship was long gone, lost in the abyss.

She shot Doyle, she shot Maura's father, or sperm donor, but still her father. She didn't shot him because she wanted to, it was her training, she went with her gut, and it cost her in the end. It hurt her to think that Maura was probably never going to speak with her again. She even thought that Maura hated her, and that's what hurt the most. She realizes that this is what Maura felt like after she got mad at her for not saying anything about her brother. Maura didn't protect Jane, and this time Jane didn't protect Maura.

Jane had a decision to make, one that would hurt even more people if she followed through with it. It's to painful for her to go on like this, she needs a clean slate, and leaving was the only way to do that. Jane sat on her couch knees crossed like always and pulls out her laptop. This was her lsat chance at getting Maura to see things her way, to talk to her one last time. Jane writes a letter explaining everything. When she finishes she saves it and does not send it she will send it tomorrow after giving Cavanaugh her resignation. She puts the laptop away, and feeds Jo, and goes to her room and lays down in bed for another sleepless night.

The next day Jane walked into the precinct, she passed by Korsac and Frost not giving them a single glance. They gave each other a sideways look and continued on with their work. She walked into Cavanaugh's office, resignation in hand.

"Rizzoli what can I do for you," he asked. Jane placed the letter down on his desk and he looked back up at her with confusion. "what's this."

"Sir I'm resigning I got a job offer in Chicago, and I'm taking it, I'm sorry it's in such short notice but I wasn't sure until last night that this is what I want to do. "

"Wait Rizzoli, what are you talking about, you can't, you can't leave, what is this all about," Cavanaugh was in utter shock not sure what to even say. "is this about Doyle and Docter Isles,"

"No Sir I just, I just need to be somewhere else right now and I need a change, that's all," Jane explained, knowing that Cavanaugh could see right through her.

" Well then I guess there's nothing else to say, except that this is a sad loss," he said.

He stood up to shake Jane's hand. "don't give them any bullshit in Chicago, Rizzoli."

Jane smiled, "thank you Sir, but I give you no promises." Jane turned to leave when Cavanagh stopped her. She turned around to meet him once more.

" Just know Rizzoli, your always welcome back, if you decide." Jane smiled and nodded and walked out of his office. Jane sat down at her desk and pulled out her laptop and pulled up her e-mail. She found her letter to Maura and sent it. She closed her laptop and removed her gun and badge. She looked at them one more time before placing them in her desk drawer.

Korsac and Frost looked at her with confusion. Jane sighed and looked at both of them. " I'm sorry guys, but I guess I should tell you now rather than later, I resigned and I'm taking a job in Chicago. And there's nothing you can say or do to make me change my mind so please don't try."

Both Korsac and Frost looked at her with a blank stare. They knew why Jane was leaving, they watched her everyday since the shooting and they knew that she wasn't the same. This is what's best for her and they hoped that she would come back. They both stood up and smiled, they reassured her in the way they looked at her. Korsac was the first to say something.

" we know Jane and we know that this is what's best, so good look in Chicago and I'm going to miss you very much, and I'll tell your mom and frankie , so don't worry." He pulled her into a big hug and kissed her cheek.

" I really don't know what to say Jane, except that I will also miss you around here, it's not going to be the same, and go kick some ass in Chicago," said Frost, he looked a little defeated. Jane was his partner and now she was leaving. Jane pulled Frost into a big hug. When they pulled away she gave them both a smile, and looked ready to cry, but held herself together.

"thank you for understanding and I'm going to miss you both so much, and I'll be safe so don't worry," she smiled. She turned to leave when Korsac stopped her.

" did you tell Maura, you were leaving," Korsac asked. She shook her head no and gave them one last smile and wave and walked out of Boston Police department.

As she drove back to her apartment all she could think about was she come and try to stop her, or if she would let her leave. When she got home she began to pack all her clothes and a few personal belongings she wamted to take. She brought them down to her car and headed back upstairs. She ate, cleaned her apartment, left a note on the counter for her mother saying that she could stay there while she was gone. When she was done she got a beer out of the fridge, fed Jo, layed down on the couch, turned on the TV and waited.

**Please Review and give feedback, my first fanfic ever so be nice. Thanks.**


	2. Chapter 2 Letting You Go

_**Chapter Two- Letting You Go**_

_**Disclaimer I do not own Rizzoli and Isles unfortunately**_

Maura sat in her office after a long day, although since the shooting everyday had been a long one. She glanced up at the clock_, 'ughh ten-thirty,'_ she thought. She started to gather her things, she took off her lab coat and hung it up, she told her forensics team they could leave and finish tomorrow. She sat back down at her desk and opened her email. She quickly searched through it getting rid of any spam mail, then; there it was an email from Jane.

She sat back from her desk, _'why is she emailing me I thought I made it clear that I didn't want to speak_ _with her,'_ she thought. After the shooting and watching the ambulance take her father away she wasn't really sure how to feel about Jane or anything. Her best friend shot her father, after she yelled at her not to; she shot the only proof she had to finding her birth mother. Jane took all that away from her, so she took herself away from Jane.

She pushed herself from Jane, she only spoke to her when it involved a case and even then she tried to avoid speaking with her. Every time Jane tried to apologize to her she would just brush her off, or push her away with harsh words. Maura was never good at being mad at Jane, because she knew what kind of person Jane was. But this time was different; Jane betrayed her, at least in her opinion, she was suppose to be her friend, she was suppose to protect her. Instead she went off and screwed her little boyfriend dean, rather than stay with her at the hospital, with her mother. Jane chose Dean, who she's only seen three times, over her and that's what hurt her the most.

She took another look at Jane's email; she shook her head, but something deep down wanted her to open the email, so she did. She took in a breath and read it.

_**Dear Maura,**_

_**I know that you don't want to speak to me or hear anything I have to say to you, but there's something I have to tell you. I know that I've apologized a million times but I'm going to say it again anyway. You have no idea how sorry I am and I know that you can't or don't want to forgive me. I ruined our friendship to the point that there is no way to rebuild it, and it hurts me so much to think about it. I'm sorry that I didn't stay with you at the hospital and that I chose Dean over you, it's probably the worst mistake I've ever made. I'm not sure how your feeling, I'm sure you're hurt and hate me and I can live with that, but I can't live with it here. I got a job offer in Chicago and I'm taking it, I resigned today and I leave early tomorrow morning. Regardless of what's happened you'll always be in my heart, even if I'm not in yours. You're my friend Maura, and I love you. I just wanted you to know that.**_

_**-Jane**_

Maura stared at the email and read it twice to make sure she understood what she was reading. Without a second thought, she shut her laptop grabbed her coat and purse and rushed to Jane's apartment.

Jane lay sprawled across the couch, with Jo lying on her stomach; there were three empty beer bottles on the table. She was a little buzzed but still coherent enough to hear the loud banging on her front door. Jo jumped off her stomach and began to bark; Jane stood up and walked to the door, yelling at Jo to shut up. She didn't bother to check who was at the door, she just opened it and when she saw who it was nearly threw up the beer in her stomach.

"Maura," Jane said, actually surprised to see her standing there. Maura waited for Jane to invite her in, Jane stepped aside and allowed Maura to come in, closing the door behind her.

When she turned around to face Maura she was immediately met with Maura hand as she stumbled backwards against the door. Jane put a hand to her cheek as the slap Maura just gave her radiated the whole side of her face. Jane looked at Maura and saw the anger in her eyes. _'She must have read the email," _Jane thought.

Maura surprised herself she had never laid a hand on anyone before let alone Jane. She put her purse down on a chair along with her jacket. She walked towards Jane and stood toe to toe with her.

"How dare you Jane Rizzoli, how dare you send me that email, did you think it would change things," Maura yelled. "Did you think I was going to come over here and beg you not to leave?"

Jane just stared at Maura, slightly afraid to speak or move. She removed her hand from her cheek and stared back at Maura, she wasn't going to allow Maura to do this to her, to tear her down even more. She looked back at Maura with the same threatening look. "No, I sent you that email to tell you that I was leaving, to tell you again about how sorry I was for choosing dean over you, for shooting Doyle, I didn't do it so that you would come over here and yell at me and put your hands on me," she spat. "And I didn't do it so that you could rip me apart even more okay; I was just trying to tell you the truth."

"The truth, that's not the truth Jane," Maura said coldly. "The truth is that you're being a coward and running away, because you can't deal with the fact that this time you screwed up and you can't do anything to fix it."

All the beers Jane drank were now setting in and she all the anger that had been building up, was coming out in an explosion. " a coward , A FUCKING COWARD, NO I'M LEAVING BECAUSE I CAN'T TAKE BEING HERE ANYMORE, IT'S BEEN MONTHS SINCE THIS WHOLE THING AND SINCE THEN YOU DON'T TALK TO ME, YOU DON'T ACKNOWLEDGE ME, YOU DON'T LOOK AT ME, YOU WON'T EVEN LET ME FRIGIN APOLOGIZE TO YOU, AND IT HURTS ME OKAY, IM JUST DONE, IM DONE TIP TOEING AROUND YOU, IM TIRED OF NOT BEING ABLE TO SLEEP BECAUSE OF MY GUILT, IM DONE FEELING LIKE A JERK, I'VE DONE EVERYTHING TO TRY AND FIX THINGS AND THERE'S NOTHING THAT I CAN FIX BECAUSE YOU ONLY SEE WHAT I DID WRONG, AND NOTHING ELSE, SO IM LEAVING TOMORROW AND IM GOING TO GO AND START NEW, WHERE I WONT HAVE TO DEAL WITH THIS BULLSHIT," Jane walked away from Maura and sat down on the couch, she put her hands over her face and let everything she had been feeling out. She cried and cried and Maura just sat there and watched. She had never seen Jane so mad, before, she had never seen her cry either. She was still completely angry, but seeing Jane break down and look so defeated it broke her on the inside. She waited for Jane to calm down and watched her wipe away her tears. Jane looked up and waited for Maura to say something, but she didn't

"Surprised to know that I have feelings too," Jane said sarcastically. "I said what I had to say, so you can just leave now, there's nothing else that can be said." Jane stood up and walked past Maura and stood by the door, "was there something else you wanted to say or did you want to slap me again."

Maura turned around to face Jane the anger that was in Maura's eyes was no longer there, you could tell by her body language she was still angry, but her eyes looked soft and calm. "I want to know how long, "

"How long what," Jane shrugged.

"How long have you loved me Jane?" Maura asked. Jane was at a standstill, completely shocked, what was she suppose to say. "How long have you been in love with me?"

"Why does it matter Maura, I'm leaving," Jane sighed.

"It matters because, that's why you're leaving, now answer the damn question Jane," Maura said irritated, "how long?"

Jane crossed her arms over her chest and sighed. She was never really good at expressing her feelings to anyone, except her family, but this was different. " I don't know Maura, since shooting myself, since Giovanni, maybe since I first saw you, there's was just something about you, and I tried to stop myself, tried to work my way around it by going out with Grant, and Casey and Dean, but it was always you, but none of that matters now." She explained defeated.

Maura tried to analyze all of it in her head but there was nothing, for once she was at a loss for words. Jane opened the door, and stepped aside for Maura. She watched as Maura grabbed her coat and jacket. Jane grabbed her arm and pulled Maura close to her.

" I'm leaving for you Maura, not for me," she said, she leaned down to her and whispered, " when you love someone you have to learn to let them go, I'm letting you go Maura." She leaned down further and brought herself face to face with Maura, she leaned forward and kissed Maura on the lips. It was soft, and full of regret it was a goodbye kiss. Jane pulled away let go of her arm and closed the door behind her. She fell down to her knees and cried once again. Maura could her Jane crying through the door, she grabbed her keys out her purse went to her car, and cried her heart out.


	3. Chapter 3 Last Chance to say Goodbye

**Chapter Three- Last Chance to say Goodbye**

**Disclaimer- Sorry for the long wait, getting ready for college and that takes awhile, so here it is, thanks for the nice reviews. I hope you enjoy and please review. Also I do not own Rizzoli and Isles.**

The airport is a great place to forget about what your thoughts, because you are so focused on what's going on around you. The rush of people leaving and entering the airport, families reuniting with each other after a long time apart. Observing others and eavesdropping on other people's conversations, however, that wasn't the case for Jane.

The airport was rather quiet at four in the morning; accept for the few people that were waiting to catch their early morning flights. She sat on a bench, left to her thoughts, which were beginning to give her a headache. _'I kissed her, I kissed Maura, how could I be so stupid_, 'she said to herself. She was mentally kicking her own ass for doing such a stupid thing. But the real question was how Maura knew that she loved her. "Because Maura knows everything," she whispered to herself.

She sighed heavily and ran her hands through her messy hair, as she continued to let her mind race. She was so deep in her own mind that she was slightly startled when she heard a very familiar voice from behind.

"Jane," said a whispered voice. She slowly turned around, and was shocked to see Maura standing there. _'not again,'_ Jane thought. Maura was still wearing the same clothes from their earlier encounter, however this time her eyes were slightly red and puffy. She looked angry, confused, sad, and calm all at the same time, if that were possible.

" Maura, what are you doing here," Jane asked a bit irritated. _'why is she doing this to me.'_

Maura just stood there and stared at Jane, unsure of what to say. "Maura," Jane pressed. Maura snapped out of her little daze and let out a breath that she had been holding in, for what seemed like forever.

"you, you kissed me and said you loved me, and now you're leaving," Maura said staring at Jane deeply, "and you say that you're leaving for me and that your letting me go."

" Maura don't do this," Jane pleaded

" do what Jane, I'm not doing anything, you're doing this," Maura said.

" I'm not doing this, not again," Jane said, her anger rising, " just go."

" no, I'm not going to go, you're going to listen, because this is probably the last time I will ever see you," Maura spat, "so you're going to listen."

Jane said nothing.

" you hurt me Jane in a way that I never thought you would, and now I don't know what to do. I thought I could trust you, but you betrayed me, you betrayed our friendship. I thought our friendship was important, that I was important. I was wrong, and I do think I can ever forgive you for that," Maura said, she was on the verge of crying, but she was not going to break down in front of Jane.

"I know you Jane, better than anyone, and you've never been one to run away from anything, so why now," Maura continued, " why now."

Jane shook her head, she was at a complete loss for words. She stood up and started to pace back and forth trying to find the right words to say.

" I'm letting you go, because for once in my life I'm giving up," Jane said, " I've tried to apologize, but the apology never gets through to you. I screwed up and I can't fix it, so what's the point anymore." Jane crossed her arms and stared Maura down.

" the point is that if you really cared about me as much as you say you do then you wouldn't be leaving, you're a fighter," Maura cried.

" I do care, but there is no fight, I lost before I had the chance, I'm doing what's best,"

" for who, for you, or for me Jane."

" for the both of us," Jane yelled, causing those who were in the airport to glance over at the two women before them, but Jane shot them a stare to mind their own business." I need to leave, because I need time to think, I need time to get over the fact that we're no longer friends. I need time to move on from you. And you need time away from me, because I see the hatred in your eyes, when you look at me, I see how your body tenses up when your around me, you hate me Maura, because I was never suppose to be the one to hurt you, I was suppose to protect you, and I didn't." Jane sobbed. " I can't deal with that, so you win."

Maura and Jane just looked at each other in complete awe, their emotions were all over the place, and either one was unsure what to say. However, Jane began to realize something, if Maura didn't care she wouldn't be here, she wouldn't be asking these questions, so why was she really here. Now it was Jane's turn to get some answers out of Maura.

" Why are you asking me all these questions, I thought that you didn't care," Jane asked.

" I don't," was her simple answer.

" see I think you do, because if you didn't then you would be here interrogating me," Jane said slyly," isn't this what you want."

Maura was silent Jane had cornered her into a wall, and Maura couldn't lie, "isn't this what you wanted," Jane repeated looking at Maura with a smirk on her face. " do you want me to leave."

Maura's heart was pounding, her mind was racing, she thought her head was about to explode, she hadn't even said anything yet and she was beginning to hyperventilate. "Maura," Jane pressed.

Maura couldn't take it anymore, she cracked, she was never good being put on the spot. " No, No okay, I don't want you to leave," Maura cried.

"why," Jane yelled, realizing that now she was beginning to cry. "Why," she sobbed.

" Because you started this, you kissed me, you told me you loved me, and….." Maura cried but stopped short.

"and, and what" Jane asked.

" and, I love you too, I stayed up all night trying to figure this out, but there was no other explanation as to why I was feeling like this, feeling like I always have. But that doesn't matter anymore, because I hate you for what you did, and I can't forgive you. So there's only one solution," Maura sobbed.

"what,"

" I'm letting you go too Jane," Maura whispered, "you're right, it's for the best."

They were both silent, they were lost within their own thoughts, both were afraid of what to do next. Their friendship was done, everything they had been through together was now coming to an end, because both of them were too stubborn to figure things out together. Over the intercom they were able to here the flights that would be leaving ' flight 142 from Boston to Chicago is now Boarding.'

This was it, their last chance to say goodbye. Jane made her way around to the other side of the bench where Maura was standing. Maura refused to look up and meet Jane's eyes. Jane cupped Maura's chin and forced her to meet her eyes.

" I need to be honest with you Maura, despite everything I need to be honest with you, and I need you to push your feelings aside, and promise me something," Jane said calmly. " There was never a job offer, and I'm not going to Chicago. I quit the force, and I don't think I'm coming back, and I need you to promise me that you won't tell anyone."

"Jane…" Maura started but Jane stopped her. " promise me Maura." Maura nodded in reply.

"thank you, now, um I need to go," Jane said. She let go of Maura's chin, and began to walk away, but Maura grabbed Jane's arm and pulled her back. She moved close to Jane, so that their faces were mere inched apart. " I need you to promise me something too," She whispered. Jane nodded letting Maura continue, " promise me that you will be safe, and not do anything reckless." Jane nodded and stared deep into Maura's eyes. " goodbye Jane," she said softly, then she leaned in a closed the small gap between her and Jane. She pressed her lips to Jane, just like Jane did when she left her apartment, but this kiss was different. It was soft, gentle, and full of guilt and sadness. She pulled away and took a step back.

They both took one last glance at each other, " goodbye Maura," Jane said. She turned around and grabbed her belongings off the bench. She gave the flight assistant her ticket and boarded the plane. There were no turning back, it was all over. What just happened between them changed everything, and now the real question was if Jane was ever going to come back.

**Okay so this was it, give me feedback on what I should do next. I hoped you all liked it so review, review, review. Thanks guys, next chapter should be posted soon. **


End file.
